I just read that your intake pipes are between the radiator and engine. You’re fighting a difficult battle having a factory hood and inner fenders. I personally don’t see you winning this battle based on my experience. I’ve built 3 of these and had inner fenders in all of them. The only success I had with a factory hood was removing the cowl seal and spacing the hood up about a 1/2” in the rear to allow the air from the fans to escape the engine bay. But that looks silly.
You’re heat soaking the intercooler, pipes, intake and heads. Air flow has to be present to get rid of the heat soak. With a proper air dam that sucks the heat out of the bay to underneath the car when driving will work, but not sitting still. When the fans engage, if you can’t feel the air flow outside of the engine bay (somewhere), then you’re destined to battle with this.
All of my cars have a cowl induction hood for a reason. Not covering the turbos and using up and forward headers just compounds the problem. You mentioned pages back that opening the hood helps a lot - there’s your sign.